Starting phenix.real_space_refine on Sun Sep 29 15:37:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/09_2024/7xyb_33516.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/09_2024/7xyb_33516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/09_2024/7xyb_33516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/09_2024/7xyb_33516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/09_2024/7xyb_33516.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyb_33516/09_2024/7xyb_33516.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 65 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 13839 2.51 5 N 4180 2.21 5 O 4374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22525 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1583 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1506 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 5, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 7672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 7672 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 445} Link IDs: {'PTRANS': 49, 'TRANS': 1140} Chain breaks: 3 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1682 Unresolved non-hydrogen angles: 2143 Unresolved non-hydrogen dihedrals: 1339 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 7, 'TYR:plan': 14, 'ASN:plan1': 21, 'TRP:plan': 2, 'ASP:plan': 47, 'PHE:plan': 18, 'GLU:plan': 63, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 970 Chain: "D" Number of atoms: 9118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 9118 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 60, 'TRANS': 1277} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1673 Unresolved non-hydrogen dihedrals: 1055 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 15, 'TRP:plan': 3, 'ASP:plan': 45, 'PHE:plan': 15, 'GLU:plan': 58, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 767 Chain: "E" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 460 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 833 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 707 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 1, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 335 Chain: "R" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 310 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "N" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 500 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "T" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 542 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.21, per 1000 atoms: 0.59 Number of scatterers: 22525 At special positions: 0 Unit cell: (142.29, 127.41, 147.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 65 15.00 Mg 1 11.99 O 4374 8.00 N 4180 7.00 C 13839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 888 " - pdb=" SG CYS D 895 " distance=2.24 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 2.8 seconds 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5886 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 47 sheets defined 41.0% alpha, 14.5% beta 25 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 8.43 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.426A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.517A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.924A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.701A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.782A pdb=" N LEU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.941A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.860A pdb=" N HIS C 169 " --> pdb=" O GLY C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 350 through 357 Processing helix chain 'C' and resid 363 through 376 Processing helix chain 'C' and resid 382 through 396 removed outlier: 3.960A pdb=" N SER C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 Processing helix chain 'C' and resid 428 through 442 Processing helix chain 'C' and resid 460 through 484 removed outlier: 3.584A pdb=" N MET C 464 " --> pdb=" O CYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 498 removed outlier: 3.537A pdb=" N ILE C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 514 Processing helix chain 'C' and resid 524 through 533 removed outlier: 3.549A pdb=" N GLU C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 548 removed outlier: 3.945A pdb=" N ALA C 548 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 560 Processing helix chain 'C' and resid 614 through 617 removed outlier: 3.565A pdb=" N ALA C 617 " --> pdb=" O ILE C 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 614 through 617' Processing helix chain 'C' and resid 661 through 665 removed outlier: 3.644A pdb=" N VAL C 665 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 Processing helix chain 'C' and resid 675 through 679 Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 708 through 717 removed outlier: 4.504A pdb=" N ASN C 712 " --> pdb=" O GLY C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 863 through 870 removed outlier: 3.525A pdb=" N LEU C 867 " --> pdb=" O GLY C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 984 Processing helix chain 'C' and resid 1021 through 1055 removed outlier: 3.646A pdb=" N GLN C1055 " --> pdb=" O ARG C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1123 removed outlier: 4.370A pdb=" N SER C1122 " --> pdb=" O LEU C1118 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C1123 " --> pdb=" O GLY C1119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1118 through 1123' Processing helix chain 'C' and resid 1126 through 1151 Processing helix chain 'C' and resid 1154 through 1167 removed outlier: 3.529A pdb=" N LEU C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1179 through 1192 removed outlier: 3.883A pdb=" N LEU C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1206 through 1217 Processing helix chain 'C' and resid 1253 through 1257 removed outlier: 3.502A pdb=" N ASP C1256 " --> pdb=" O LEU C1253 " (cutoff:3.500A) Processing helix chain 'C' and resid 1286 through 1296 Processing helix chain 'C' and resid 1299 through 1308 Processing helix chain 'C' and resid 1312 through 1325 removed outlier: 3.952A pdb=" N THR C1317 " --> pdb=" O VAL C1313 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS C1318 " --> pdb=" O ASN C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1335 through 1348 removed outlier: 3.581A pdb=" N ASN C1339 " --> pdb=" O PRO C1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.895A pdb=" N ILE D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 193 through 208 Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.710A pdb=" N VAL D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.525A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.900A pdb=" N TRP D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 410 " --> pdb=" O PRO D 406 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.730A pdb=" N GLN D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 635 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.295A pdb=" N ARG D 652 " --> pdb=" O ASP D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.865A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1051 through 1055 removed outlier: 3.653A pdb=" N THR D1054 " --> pdb=" O ASP D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.837A pdb=" N ILE D1220 " --> pdb=" O ASN D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.560A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.308A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1292 removed outlier: 3.506A pdb=" N LEU D1292 " --> pdb=" O GLU D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.991A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.517A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1375 Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 17 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.549A pdb=" N PHE G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 69 Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 86 through 101 Processing helix chain 'G' and resid 105 through 120 Processing helix chain 'G' and resid 126 through 135 Processing helix chain 'G' and resid 137 through 171 removed outlier: 4.287A pdb=" N GLU G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) Proline residue: G 166 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 6.429A pdb=" N ALA A 146 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL A 56 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY A 148 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N CYS A 54 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 170 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.567A pdb=" N ALA A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.665A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 61 removed outlier: 6.808A pdb=" N LYS B 144 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 59 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS B 142 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.568A pdb=" N ALA B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.978A pdb=" N LYS C 13 " --> pdb=" O ALA C1198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 70 through 79 removed outlier: 5.312A pdb=" N LEU C 72 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE C 107 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TYR C 74 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG C 105 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 76 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 103 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 119 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 70 through 79 removed outlier: 5.312A pdb=" N LEU C 72 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE C 107 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TYR C 74 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG C 105 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 76 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 103 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB6, first strand: chain 'C' and resid 456 through 458 Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.557A pdb=" N LEU C 188 " --> pdb=" O ILE C 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AB9, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AC1, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AC2, first strand: chain 'C' and resid 755 through 757 removed outlier: 6.941A pdb=" N ARG C 736 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL C 732 " --> pdb=" O ARG C 736 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 738 " --> pdb=" O ASP C 730 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 762 through 763 Processing sheet with id=AC4, first strand: chain 'C' and resid 794 through 795 Processing sheet with id=AC5, first strand: chain 'C' and resid 1083 through 1084 removed outlier: 4.699A pdb=" N THR C1241 " --> pdb=" O PHE C 809 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS C 822 " --> pdb=" O VAL C1114 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE C 821 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C1096 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 823 " --> pdb=" O ILE C1096 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1083 through 1084 Processing sheet with id=AC7, first strand: chain 'C' and resid 835 through 844 removed outlier: 4.074A pdb=" N ASP C 935 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA C1072 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL C 933 " --> pdb=" O ALA C1072 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS C1074 " --> pdb=" O GLY C 931 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N GLY C 931 " --> pdb=" O LYS C1074 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 854 through 855 removed outlier: 3.919A pdb=" N GLU C 854 " --> pdb=" O VAL C 892 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 889 removed outlier: 6.235A pdb=" N LEU C 923 " --> pdb=" O LEU C 888 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.553A pdb=" N HIS C1259 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.553A pdb=" N HIS C1259 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1350 through 1351 Processing sheet with id=AD4, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.020A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.794A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AD8, first strand: chain 'D' and resid 253 through 255 Processing sheet with id=AD9, first strand: chain 'D' and resid 316 through 317 removed outlier: 4.056A pdb=" N THR D 317 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 6.842A pdb=" N PHE D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N ASN D 553 " --> pdb=" O PHE D 527 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY D 558 " --> pdb=" O GLN D 562 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLN D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 991 through 996 removed outlier: 3.876A pdb=" N GLU D 993 " --> pdb=" O VAL D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AE6, first strand: chain 'D' and resid 1033 through 1034 removed outlier: 3.578A pdb=" N GLY D1033 " --> pdb=" O VAL D1115 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1036 through 1038 Processing sheet with id=AE8, first strand: chain 'D' and resid 1046 through 1047 removed outlier: 3.712A pdb=" N ILE D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D1107 " --> pdb=" O ILE D1059 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1155 through 1156 Processing sheet with id=AF1, first strand: chain 'D' and resid 1172 through 1174 Processing sheet with id=AF2, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 7.027A pdb=" N LYS D1301 " --> pdb=" O SER D1267 " (cutoff:3.500A) 1103 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 11.49 Time building geometry restraints manager: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5054 1.33 - 1.45: 4674 1.45 - 1.57: 12960 1.57 - 1.69: 126 1.69 - 1.82: 115 Bond restraints: 22929 Sorted by residual: bond pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.44e+00 bond pdb=" N LEU G 45 " pdb=" CA LEU G 45 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.30e-02 5.92e+03 7.00e+00 bond pdb=" N ILE G 42 " pdb=" CA ILE G 42 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.90e+00 bond pdb=" O3' DG N 119 " pdb=" P DG N 120 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.68e+00 bond pdb=" N GLY C 851 " pdb=" CA GLY C 851 " ideal model delta sigma weight residual 1.443 1.477 -0.035 1.37e-02 5.33e+03 6.48e+00 ... (remaining 22924 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 31222 2.94 - 5.88: 263 5.88 - 8.82: 30 8.82 - 11.76: 8 11.76 - 14.70: 1 Bond angle restraints: 31524 Sorted by residual: angle pdb=" C THR D 43 " pdb=" CA THR D 43 " pdb=" CB THR D 43 " ideal model delta sigma weight residual 116.53 101.83 14.70 1.47e+00 4.63e-01 1.00e+02 angle pdb=" N LYS C1277 " pdb=" CA LYS C1277 " pdb=" C LYS C1277 " ideal model delta sigma weight residual 111.28 103.79 7.49 1.09e+00 8.42e-01 4.72e+01 angle pdb=" O3' U R 61 " pdb=" C3' U R 61 " pdb=" C2' U R 61 " ideal model delta sigma weight residual 109.50 119.16 -9.66 1.50e+00 4.44e-01 4.14e+01 angle pdb=" N GLU G 35 " pdb=" CA GLU G 35 " pdb=" C GLU G 35 " ideal model delta sigma weight residual 113.41 105.70 7.71 1.22e+00 6.72e-01 3.99e+01 angle pdb=" N ARG G 34 " pdb=" CA ARG G 34 " pdb=" C ARG G 34 " ideal model delta sigma weight residual 113.20 106.07 7.13 1.21e+00 6.83e-01 3.48e+01 ... (remaining 31519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 12169 17.89 - 35.78: 1070 35.78 - 53.67: 357 53.67 - 71.56: 118 71.56 - 89.45: 13 Dihedral angle restraints: 13727 sinusoidal: 4624 harmonic: 9103 Sorted by residual: dihedral pdb=" CB CYS D 888 " pdb=" SG CYS D 888 " pdb=" SG CYS D 895 " pdb=" CB CYS D 895 " ideal model delta sinusoidal sigma weight residual -86.00 -171.12 85.12 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CA ALA G 27 " pdb=" C ALA G 27 " pdb=" N MET G 28 " pdb=" CA MET G 28 " ideal model delta harmonic sigma weight residual 180.00 155.36 24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" C THR D 43 " pdb=" N THR D 43 " pdb=" CA THR D 43 " pdb=" CB THR D 43 " ideal model delta harmonic sigma weight residual -122.00 -111.17 -10.83 0 2.50e+00 1.60e-01 1.87e+01 ... (remaining 13724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3268 0.061 - 0.122: 522 0.122 - 0.183: 42 0.183 - 0.245: 6 0.245 - 0.306: 4 Chirality restraints: 3842 Sorted by residual: chirality pdb=" CA THR D 43 " pdb=" N THR D 43 " pdb=" C THR D 43 " pdb=" CB THR D 43 " both_signs ideal model delta sigma weight residual False 2.53 2.83 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA LYS C1277 " pdb=" N LYS C1277 " pdb=" C LYS C1277 " pdb=" CB LYS C1277 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ILE D 44 " pdb=" N ILE D 44 " pdb=" C ILE D 44 " pdb=" CB ILE D 44 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3839 not shown) Planarity restraints: 3969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 42 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C GLU D 42 " 0.049 2.00e-02 2.50e+03 pdb=" O GLU D 42 " -0.019 2.00e-02 2.50e+03 pdb=" N THR D 43 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 846 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C ARG C 846 " -0.049 2.00e-02 2.50e+03 pdb=" O ARG C 846 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP C 847 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 48 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C THR D 48 " 0.048 2.00e-02 2.50e+03 pdb=" O THR D 48 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE D 49 " -0.017 2.00e-02 2.50e+03 ... (remaining 3966 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 248 2.55 - 3.13: 18935 3.13 - 3.72: 38051 3.72 - 4.31: 47327 4.31 - 4.90: 76985 Nonbonded interactions: 181546 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1601 " model vdw 1.956 2.170 nonbonded pdb=" O3' A R 70 " pdb="MG MG D1601 " model vdw 1.986 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1601 " model vdw 1.994 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1601 " model vdw 2.083 2.170 nonbonded pdb=" N GLN C 839 " pdb=" OE1 GLN C 839 " model vdw 2.192 3.120 ... (remaining 181541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 15 or (resid 16 and (name N or name \ CA or name C or name O or name CB )) or resid 17 through 57 or (resid 58 throug \ h 62 and (name N or name CA or name C or name O or name CB )) or resid 63 or (re \ sid 64 through 66 and (name N or name CA or name C or name O or name CB )) or re \ sid 67 through 74 or (resid 75 and (name N or name CA or name C or name O or nam \ e CB )) or resid 76 through 79 or (resid 80 and (name N or name CA or name C or \ name O or name CB )) or resid 81 through 89 or (resid 90 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2)) or resid 91 through 92 \ or (resid 93 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 4 or (resid 95 and (name N or name CA or name C or name O or name CB or name CG \ )) or resid 96 through 104 or (resid 105 and (name N or name CA or name C or nam \ e O or name CB )) or resid 109 through 113 or (resid 114 and (name N or name CA \ or name C or name O or name CB )) or resid 115 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 120 through 134 or re \ sid 139 through 141 or (resid 142 and (name N or name CA or name C or name O or \ name CB )) or resid 143 through 157 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 182 or (resid 183 and (name N or \ name CA or name C or name O or name CB )) or resid 184 through 217 or (resid 21 \ 8 through 220 and (name N or name CA or name C or name O or name CB )) or resid \ 221 through 230)) selection = (chain 'B' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or resid 15 through 25 or (resid \ 26 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2)) or resid 27 through 31 or (resid 32 and (name N or name CA or name C or name \ O or name CB )) or resid 33 through 71 or (resid 72 and (name N or name CA or n \ ame C or name O or name CB )) or resid 73 through 116 or (resid 117 and (name N \ or name CA or name C or name O or name CB )) or resid 118 through 126 or (resid \ 127 and (name N or name CA or name C or name O or name CB or name CG )) or resid \ 128 through 139 or (resid 140 and (name N or name CA or name C or name O or nam \ e CB or name CG )) or resid 141 through 151 or (resid 152 and (name N or name CA \ or name C or name O or name CB )) or resid 153 through 193 or (resid 194 throug \ h 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thro \ ugh 212 or (resid 213 through 215 and (name N or name CA or name C or name O or \ name CB )) or resid 216 through 230)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 58.590 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22929 Z= 0.306 Angle : 0.747 14.698 31524 Z= 0.444 Chirality : 0.045 0.306 3842 Planarity : 0.004 0.052 3969 Dihedral : 16.728 89.453 7838 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.96 % Rotamer: Outliers : 0.62 % Allowed : 23.17 % Favored : 76.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 3157 helix: 1.23 (0.16), residues: 1182 sheet: -1.23 (0.25), residues: 401 loop : -1.31 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 812 HIS 0.014 0.002 HIS A 37 PHE 0.031 0.001 PHE A 35 TYR 0.017 0.001 TYR D1241 ARG 0.028 0.001 ARG D1149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping REVERT: C 690 MET cc_start: 0.9091 (mpp) cc_final: 0.8712 (mpp) REVERT: C 810 MET cc_start: 0.8635 (ttp) cc_final: 0.8390 (ppp) REVERT: D 298 MET cc_start: 0.8631 (ptp) cc_final: 0.8373 (ptp) outliers start: 11 outliers final: 6 residues processed: 143 average time/residue: 0.2950 time to fit residues: 70.9484 Evaluate side-chains 132 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 46 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 0.9980 chunk 242 optimal weight: 7.9990 chunk 134 optimal weight: 0.3980 chunk 82 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 290 optimal weight: 0.4980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN D 277 ASN D 921 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22929 Z= 0.199 Angle : 0.581 8.033 31524 Z= 0.311 Chirality : 0.042 0.153 3842 Planarity : 0.004 0.042 3969 Dihedral : 14.338 85.284 4139 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 2.59 % Allowed : 19.29 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3157 helix: 1.64 (0.15), residues: 1196 sheet: -1.18 (0.26), residues: 373 loop : -1.16 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 868 HIS 0.006 0.001 HIS A 37 PHE 0.014 0.001 PHE C 647 TYR 0.017 0.001 TYR C1244 ARG 0.006 0.001 ARG C 773 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 134 time to evaluate : 2.302 Fit side-chains revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping REVERT: A 35 PHE cc_start: 0.9024 (t80) cc_final: 0.8729 (t80) REVERT: A 76 GLU cc_start: 0.9200 (mp0) cc_final: 0.8925 (mp0) REVERT: A 142 LYS cc_start: 0.9468 (mmmm) cc_final: 0.9198 (mmmt) REVERT: A 145 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8383 (t) REVERT: C 134 MET cc_start: 0.8891 (tmm) cc_final: 0.8624 (tmm) REVERT: C 810 MET cc_start: 0.8618 (ttp) cc_final: 0.8383 (ppp) REVERT: C 1148 MET cc_start: 0.9065 (ptp) cc_final: 0.8685 (ptp) REVERT: C 1247 MET cc_start: 0.9374 (mmm) cc_final: 0.9031 (mmm) REVERT: D 130 MET cc_start: 0.9098 (ppp) cc_final: 0.8877 (ppp) REVERT: D 147 ILE cc_start: 0.7395 (mm) cc_final: 0.7168 (mm) REVERT: D 298 MET cc_start: 0.8629 (ptp) cc_final: 0.8262 (ptp) REVERT: D 549 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8828 (mppt) REVERT: D 743 MET cc_start: 0.8506 (ppp) cc_final: 0.8255 (tmm) REVERT: E 30 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9061 (mm) outliers start: 43 outliers final: 15 residues processed: 171 average time/residue: 0.2943 time to fit residues: 84.7980 Evaluate side-chains 146 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1213 MET Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 46 PRO Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 0.0670 chunk 90 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 197 optimal weight: 40.0000 chunk 80 optimal weight: 4.9990 chunk 291 optimal weight: 10.0000 chunk 314 optimal weight: 6.9990 chunk 259 optimal weight: 30.0000 chunk 288 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 188 ASN B 116 GLN B 140 ASN C 467 ASN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22929 Z= 0.270 Angle : 0.582 7.511 31524 Z= 0.306 Chirality : 0.041 0.156 3842 Planarity : 0.004 0.043 3969 Dihedral : 14.094 87.350 4134 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.57 % Favored : 94.33 % Rotamer: Outliers : 3.64 % Allowed : 20.02 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3157 helix: 1.84 (0.15), residues: 1205 sheet: -1.17 (0.25), residues: 390 loop : -1.06 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 33 HIS 0.006 0.001 HIS D 104 PHE 0.012 0.001 PHE C 511 TYR 0.016 0.001 TYR C1244 ARG 0.006 0.000 ARG C 773 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 131 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8763 (t80) REVERT: A 142 LYS cc_start: 0.9441 (mmmm) cc_final: 0.9146 (mmmt) REVERT: B 206 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8497 (p) REVERT: C 134 MET cc_start: 0.8872 (tmm) cc_final: 0.8626 (tmm) REVERT: C 810 MET cc_start: 0.8727 (ttp) cc_final: 0.8385 (ppp) REVERT: C 1181 ASP cc_start: 0.8992 (m-30) cc_final: 0.8732 (p0) REVERT: C 1247 MET cc_start: 0.9337 (mmm) cc_final: 0.9058 (mmm) REVERT: D 130 MET cc_start: 0.9065 (ppp) cc_final: 0.8136 (ppp) REVERT: D 298 MET cc_start: 0.8698 (ptp) cc_final: 0.8355 (ptp) REVERT: D 724 MET cc_start: 0.9329 (mpp) cc_final: 0.8895 (mpp) REVERT: D 816 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8610 (p) REVERT: E 30 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9060 (mm) outliers start: 59 outliers final: 33 residues processed: 182 average time/residue: 0.2867 time to fit residues: 87.8934 Evaluate side-chains 163 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 829 GLN Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1213 MET Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 30 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 0.6980 chunk 218 optimal weight: 10.0000 chunk 151 optimal weight: 40.0000 chunk 32 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 292 optimal weight: 5.9990 chunk 309 optimal weight: 30.0000 chunk 152 optimal weight: 30.0000 chunk 276 optimal weight: 50.0000 chunk 83 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN C 771 ASN C 804 ASN ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22929 Z= 0.268 Angle : 0.575 10.225 31524 Z= 0.301 Chirality : 0.041 0.153 3842 Planarity : 0.004 0.041 3969 Dihedral : 14.035 89.509 4132 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.51 % Favored : 94.39 % Rotamer: Outliers : 4.13 % Allowed : 21.26 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 3157 helix: 1.90 (0.15), residues: 1204 sheet: -1.24 (0.25), residues: 391 loop : -0.99 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 812 HIS 0.007 0.001 HIS C 556 PHE 0.013 0.001 PHE C 160 TYR 0.016 0.001 TYR C1244 ARG 0.007 0.000 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 130 time to evaluate : 2.339 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9160 (mp0) cc_final: 0.8898 (mp0) REVERT: C 658 MET cc_start: 0.8800 (tmm) cc_final: 0.8594 (tmm) REVERT: C 810 MET cc_start: 0.8737 (ttp) cc_final: 0.8386 (ppp) REVERT: C 1148 MET cc_start: 0.9068 (ptm) cc_final: 0.8709 (ptp) REVERT: C 1247 MET cc_start: 0.9340 (mmm) cc_final: 0.9029 (mmm) REVERT: C 1248 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9012 (mt) REVERT: D 102 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7359 (mtp) REVERT: D 130 MET cc_start: 0.9052 (ppp) cc_final: 0.8297 (ppp) REVERT: D 298 MET cc_start: 0.8736 (ptp) cc_final: 0.8381 (ptp) REVERT: D 330 MET cc_start: 0.9067 (mmp) cc_final: 0.8834 (mmp) REVERT: D 724 MET cc_start: 0.9287 (mpp) cc_final: 0.8861 (mpp) REVERT: D 816 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8587 (p) REVERT: E 25 LYS cc_start: 0.9758 (mmmm) cc_final: 0.9510 (mmmt) REVERT: E 30 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8997 (mm) outliers start: 67 outliers final: 42 residues processed: 189 average time/residue: 0.2705 time to fit residues: 88.2226 Evaluate side-chains 170 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 124 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1213 MET Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1275 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 40.0000 chunk 175 optimal weight: 40.0000 chunk 4 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 263 optimal weight: 50.0000 chunk 213 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 157 optimal weight: 50.0000 chunk 277 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 overall best weight: 6.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN B 193 GLN C 804 ASN ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 HIS ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22929 Z= 0.321 Angle : 0.597 11.586 31524 Z= 0.313 Chirality : 0.042 0.172 3842 Planarity : 0.004 0.042 3969 Dihedral : 14.035 87.370 4132 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.76 % Rotamer: Outliers : 4.50 % Allowed : 20.58 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3157 helix: 1.82 (0.15), residues: 1218 sheet: -1.22 (0.26), residues: 374 loop : -1.07 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 812 HIS 0.008 0.001 HIS C 556 PHE 0.013 0.001 PHE C 160 TYR 0.017 0.002 TYR D 631 ARG 0.005 0.000 ARG C 773 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 123 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9176 (mp0) cc_final: 0.8880 (mp0) REVERT: A 142 LYS cc_start: 0.9494 (mmmm) cc_final: 0.9164 (mmmt) REVERT: B 46 ILE cc_start: 0.9797 (OUTLIER) cc_final: 0.9559 (tt) REVERT: C 810 MET cc_start: 0.8705 (ttp) cc_final: 0.8350 (ppp) REVERT: C 1148 MET cc_start: 0.9021 (ptm) cc_final: 0.8665 (ptp) REVERT: C 1247 MET cc_start: 0.9308 (mmm) cc_final: 0.8944 (mmm) REVERT: C 1248 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8973 (mt) REVERT: D 102 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7287 (mtp) REVERT: D 330 MET cc_start: 0.9090 (mmp) cc_final: 0.8879 (mmp) REVERT: D 724 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8929 (mpp) REVERT: D 816 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8558 (p) REVERT: E 25 LYS cc_start: 0.9776 (mmmm) cc_final: 0.9523 (mmmt) REVERT: E 30 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9044 (mm) outliers start: 73 outliers final: 49 residues processed: 186 average time/residue: 0.2773 time to fit residues: 88.0491 Evaluate side-chains 179 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 124 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1213 MET Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1275 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 30 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 2.9990 chunk 278 optimal weight: 8.9990 chunk 61 optimal weight: 40.0000 chunk 181 optimal weight: 0.6980 chunk 76 optimal weight: 20.0000 chunk 309 optimal weight: 40.0000 chunk 257 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 162 optimal weight: 30.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN B 140 ASN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 HIS ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22929 Z= 0.258 Angle : 0.565 11.798 31524 Z= 0.297 Chirality : 0.041 0.156 3842 Planarity : 0.004 0.043 3969 Dihedral : 13.948 85.935 4132 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.32 % Favored : 94.58 % Rotamer: Outliers : 4.56 % Allowed : 20.70 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 3157 helix: 1.91 (0.15), residues: 1214 sheet: -1.20 (0.26), residues: 394 loop : -0.98 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 868 HIS 0.007 0.001 HIS C 556 PHE 0.010 0.001 PHE C 511 TYR 0.016 0.001 TYR D 631 ARG 0.005 0.000 ARG C 740 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 128 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9213 (mp0) cc_final: 0.8944 (mp0) REVERT: A 142 LYS cc_start: 0.9433 (mmmm) cc_final: 0.8815 (mmmt) REVERT: B 35 PHE cc_start: 0.9158 (m-80) cc_final: 0.8936 (m-80) REVERT: B 46 ILE cc_start: 0.9760 (OUTLIER) cc_final: 0.9542 (tt) REVERT: B 51 MET cc_start: 0.9003 (mmt) cc_final: 0.8732 (mmm) REVERT: C 810 MET cc_start: 0.8680 (ttp) cc_final: 0.8451 (ppp) REVERT: C 1247 MET cc_start: 0.9320 (mmm) cc_final: 0.8909 (mmm) REVERT: C 1248 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9087 (mt) REVERT: D 60 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7370 (mptt) REVERT: D 102 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7356 (mtp) REVERT: D 130 MET cc_start: 0.8968 (ppp) cc_final: 0.7816 (ppp) REVERT: D 330 MET cc_start: 0.9092 (mmp) cc_final: 0.8866 (mmp) REVERT: D 816 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8539 (p) REVERT: D 1260 MET cc_start: 0.8057 (mtp) cc_final: 0.7803 (mtp) REVERT: E 25 LYS cc_start: 0.9784 (mmmm) cc_final: 0.9529 (mmmt) REVERT: E 30 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9068 (mm) outliers start: 74 outliers final: 49 residues processed: 193 average time/residue: 0.2739 time to fit residues: 89.4952 Evaluate side-chains 179 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 124 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain D residue 1275 ILE Chi-restraints excluded: chain E residue 30 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 260 optimal weight: 50.0000 chunk 172 optimal weight: 3.9990 chunk 308 optimal weight: 50.0000 chunk 193 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN B 226 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22929 Z= 0.302 Angle : 0.597 11.768 31524 Z= 0.311 Chirality : 0.041 0.162 3842 Planarity : 0.004 0.044 3969 Dihedral : 13.947 86.490 4132 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.05 % Favored : 93.85 % Rotamer: Outliers : 4.37 % Allowed : 21.69 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 3157 helix: 1.87 (0.15), residues: 1217 sheet: -1.19 (0.26), residues: 388 loop : -0.98 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 868 HIS 0.008 0.001 HIS C 556 PHE 0.011 0.001 PHE C 160 TYR 0.016 0.001 TYR D 631 ARG 0.007 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 125 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9218 (mp0) cc_final: 0.8937 (mp0) REVERT: B 35 PHE cc_start: 0.9183 (m-80) cc_final: 0.8923 (m-80) REVERT: B 46 ILE cc_start: 0.9755 (OUTLIER) cc_final: 0.9526 (tt) REVERT: B 51 MET cc_start: 0.9023 (mmt) cc_final: 0.8746 (mmm) REVERT: C 658 MET cc_start: 0.8823 (ppp) cc_final: 0.8488 (tmm) REVERT: C 690 MET cc_start: 0.8967 (mtt) cc_final: 0.8578 (mtt) REVERT: C 810 MET cc_start: 0.8691 (ttp) cc_final: 0.8461 (ppp) REVERT: C 1247 MET cc_start: 0.9322 (mmm) cc_final: 0.8914 (mmm) REVERT: C 1248 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9050 (mt) REVERT: D 60 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7551 (mmtm) REVERT: D 102 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7674 (ttp) REVERT: D 130 MET cc_start: 0.8964 (ppp) cc_final: 0.7946 (ppp) REVERT: D 330 MET cc_start: 0.9123 (mmp) cc_final: 0.8890 (mmp) REVERT: D 816 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8547 (p) REVERT: E 25 LYS cc_start: 0.9785 (mmmm) cc_final: 0.9529 (mmmt) REVERT: E 30 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9102 (mm) outliers start: 71 outliers final: 55 residues processed: 189 average time/residue: 0.2748 time to fit residues: 89.6524 Evaluate side-chains 182 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 121 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1083 MET Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 30 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 0.6980 chunk 123 optimal weight: 40.0000 chunk 184 optimal weight: 30.0000 chunk 92 optimal weight: 30.0000 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1078 GLN ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22929 Z= 0.178 Angle : 0.557 13.059 31524 Z= 0.289 Chirality : 0.041 0.162 3842 Planarity : 0.003 0.045 3969 Dihedral : 13.797 86.160 4132 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 2.71 % Allowed : 23.66 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 3157 helix: 2.00 (0.15), residues: 1208 sheet: -1.13 (0.27), residues: 366 loop : -0.84 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 868 HIS 0.005 0.001 HIS C 556 PHE 0.008 0.001 PHE C 511 TYR 0.013 0.001 TYR D1241 ARG 0.006 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 131 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9214 (mp0) cc_final: 0.8971 (mp0) REVERT: B 35 PHE cc_start: 0.9083 (m-80) cc_final: 0.8817 (m-80) REVERT: B 51 MET cc_start: 0.9031 (mmt) cc_final: 0.8721 (mmm) REVERT: C 658 MET cc_start: 0.8808 (ppp) cc_final: 0.8495 (tmm) REVERT: C 690 MET cc_start: 0.8963 (mtt) cc_final: 0.8645 (mtt) REVERT: C 1148 MET cc_start: 0.9180 (ptp) cc_final: 0.8862 (ptp) REVERT: C 1247 MET cc_start: 0.9355 (mmm) cc_final: 0.9022 (mmm) REVERT: C 1248 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9157 (mt) REVERT: D 102 MET cc_start: 0.8296 (mtp) cc_final: 0.7732 (ttp) REVERT: D 130 MET cc_start: 0.8939 (ppp) cc_final: 0.7958 (ppp) REVERT: D 330 MET cc_start: 0.9091 (mmp) cc_final: 0.8837 (mmp) REVERT: D 816 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8467 (p) REVERT: D 822 MET cc_start: 0.9018 (ptt) cc_final: 0.8602 (ppp) REVERT: E 25 LYS cc_start: 0.9788 (mmmm) cc_final: 0.9538 (mmmt) REVERT: E 30 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9063 (mm) outliers start: 44 outliers final: 31 residues processed: 168 average time/residue: 0.2928 time to fit residues: 84.4847 Evaluate side-chains 162 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 30 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 6.9990 chunk 295 optimal weight: 20.0000 chunk 269 optimal weight: 7.9990 chunk 287 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 259 optimal weight: 0.0770 chunk 271 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22929 Z= 0.256 Angle : 0.585 13.040 31524 Z= 0.301 Chirality : 0.041 0.162 3842 Planarity : 0.003 0.044 3969 Dihedral : 13.790 86.667 4132 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.43 % Rotamer: Outliers : 2.71 % Allowed : 23.66 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 3157 helix: 2.02 (0.16), residues: 1204 sheet: -1.18 (0.27), residues: 385 loop : -0.80 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 41 HIS 0.007 0.001 HIS C 556 PHE 0.011 0.001 PHE C 394 TYR 0.015 0.001 TYR D1241 ARG 0.005 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9218 (mp0) cc_final: 0.8971 (mp0) REVERT: B 51 MET cc_start: 0.9014 (mmt) cc_final: 0.8768 (mmm) REVERT: C 690 MET cc_start: 0.8934 (mtt) cc_final: 0.8406 (mpp) REVERT: C 1247 MET cc_start: 0.9285 (mmm) cc_final: 0.8818 (mmm) REVERT: C 1248 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9144 (mt) REVERT: D 60 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7677 (mmtm) REVERT: D 102 MET cc_start: 0.8311 (mtp) cc_final: 0.7664 (ttp) REVERT: D 130 MET cc_start: 0.8940 (ppp) cc_final: 0.7942 (ppp) REVERT: D 330 MET cc_start: 0.9118 (mmp) cc_final: 0.8857 (mmp) REVERT: D 596 MET cc_start: 0.8470 (tpp) cc_final: 0.7459 (mpp) REVERT: D 816 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8465 (p) REVERT: D 822 MET cc_start: 0.9045 (ptt) cc_final: 0.8613 (ppp) REVERT: E 25 LYS cc_start: 0.9784 (mmmm) cc_final: 0.9549 (mmmt) outliers start: 44 outliers final: 34 residues processed: 164 average time/residue: 0.2789 time to fit residues: 79.1626 Evaluate side-chains 159 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 122 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 3.9990 chunk 303 optimal weight: 0.5980 chunk 185 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 293 optimal weight: 50.0000 chunk 253 optimal weight: 40.0000 chunk 26 optimal weight: 20.0000 chunk 196 optimal weight: 0.9990 chunk 155 optimal weight: 30.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22929 Z= 0.198 Angle : 0.578 14.479 31524 Z= 0.296 Chirality : 0.041 0.177 3842 Planarity : 0.003 0.043 3969 Dihedral : 13.722 86.460 4132 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 2.34 % Allowed : 24.15 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 3157 helix: 2.00 (0.15), residues: 1209 sheet: -1.23 (0.27), residues: 378 loop : -0.76 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 868 HIS 0.006 0.001 HIS C 556 PHE 0.008 0.001 PHE C 511 TYR 0.014 0.001 TYR D1241 ARG 0.005 0.000 ARG D 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8466 (t80) REVERT: A 75 GLN cc_start: 0.9214 (tp40) cc_final: 0.8963 (tp40) REVERT: A 76 GLU cc_start: 0.9212 (mp0) cc_final: 0.8960 (mp0) REVERT: A 142 LYS cc_start: 0.9311 (mmmm) cc_final: 0.8931 (mmmt) REVERT: B 51 MET cc_start: 0.9016 (mmt) cc_final: 0.8328 (mmm) REVERT: C 134 MET cc_start: 0.8698 (tmm) cc_final: 0.8286 (tmm) REVERT: C 690 MET cc_start: 0.8922 (mtt) cc_final: 0.8363 (mpp) REVERT: C 1247 MET cc_start: 0.9287 (mmm) cc_final: 0.8861 (mmm) REVERT: C 1248 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9132 (mt) REVERT: D 102 MET cc_start: 0.8290 (mtp) cc_final: 0.7419 (mtp) REVERT: D 130 MET cc_start: 0.8908 (ppp) cc_final: 0.7899 (ppp) REVERT: D 330 MET cc_start: 0.9105 (mmp) cc_final: 0.8849 (mmp) REVERT: D 596 MET cc_start: 0.8462 (tpp) cc_final: 0.7486 (mpp) REVERT: D 816 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8468 (p) REVERT: D 822 MET cc_start: 0.9004 (ptt) cc_final: 0.8580 (ppp) REVERT: E 25 LYS cc_start: 0.9769 (mmmm) cc_final: 0.9559 (mmmt) outliers start: 38 outliers final: 34 residues processed: 160 average time/residue: 0.2809 time to fit residues: 77.4768 Evaluate side-chains 161 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1191 LEU Chi-restraints excluded: chain C residue 1195 VAL Chi-restraints excluded: chain C residue 1248 LEU Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 0.5980 chunk 270 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 254 optimal weight: 50.0000 chunk 106 optimal weight: 10.0000 chunk 261 optimal weight: 50.0000 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.042553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.033812 restraints weight = 191148.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034603 restraints weight = 115546.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.035145 restraints weight = 79131.313| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22929 Z= 0.227 Angle : 0.590 13.723 31524 Z= 0.302 Chirality : 0.041 0.188 3842 Planarity : 0.003 0.042 3969 Dihedral : 13.700 86.602 4132 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 2.77 % Allowed : 24.09 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 3157 helix: 2.06 (0.16), residues: 1198 sheet: -1.21 (0.27), residues: 384 loop : -0.69 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 868 HIS 0.006 0.001 HIS C 556 PHE 0.010 0.001 PHE C 394 TYR 0.015 0.001 TYR D1241 ARG 0.005 0.000 ARG D 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3372.35 seconds wall clock time: 61 minutes 32.37 seconds (3692.37 seconds total)